#include <deal.II/lac/petsc_matrix_free.h>

Inheritance diagram for PETScWrappers::MatrixFree:

Public Member Functions
	MatrixFree ()

	MatrixFree (const MPI_Comm &communicator, const unsigned int m, const unsigned int n, const unsigned int local_rows, const unsigned int local_columns)

	MatrixFree (const MPI_Comm &communicator, const unsigned int m, const unsigned int n, const std::vector< unsigned int > &local_rows_per_process, const std::vector< unsigned int > &local_columns_per_process, const unsigned int this_process)

	MatrixFree (const unsigned int m, const unsigned int n, const unsigned int local_rows, const unsigned int local_columns)

	MatrixFree (const unsigned int m, const unsigned int n, const std::vector< unsigned int > &local_rows_per_process, const std::vector< unsigned int > &local_columns_per_process, const unsigned int this_process)

void	reinit (const MPI_Comm &communicator, const unsigned int m, const unsigned int n, const unsigned int local_rows, const unsigned int local_columns)

void	reinit (const MPI_Comm &communicator, const unsigned int m, const unsigned int n, const std::vector< unsigned int > &local_rows_per_process, const std::vector< unsigned int > &local_columns_per_process, const unsigned int this_process)

void	reinit (const unsigned int m, const unsigned int n, const unsigned int local_rows, const unsigned int local_columns)

void	reinit (const unsigned int m, const unsigned int n, const std::vector< unsigned int > &local_rows_per_process, const std::vector< unsigned int > &local_columns_per_process, const unsigned int this_process)

void	clear ()

const MPI_Comm &	get_mpi_communicator () const override

virtual void	vmult (VectorBase &dst, const VectorBase &src) const =0

virtual void	Tvmult (VectorBase &dst, const VectorBase &src) const =0

virtual void	vmult_add (VectorBase &dst, const VectorBase &src) const =0

virtual void	Tvmult_add (VectorBase &dst, const VectorBase &src) const =0

virtual void	vmult (Vec &dst, const Vec &src) const

Public Member Functions inherited from PETScWrappers::MatrixBase
	MatrixBase ()

	MatrixBase (const MatrixBase &)=delete

MatrixBase &	operator= (const MatrixBase &)=delete

virtual	~MatrixBase () override

MatrixBase &	operator= (const value_type d)

void	clear ()

void	set (const size_type i, const size_type j, const PetscScalar value)

void	set (const std::vector< size_type > &indices, const FullMatrix< PetscScalar > &full_matrix, const bool elide_zero_values=false)

void	set (const std::vector< size_type > &row_indices, const std::vector< size_type > &col_indices, const FullMatrix< PetscScalar > &full_matrix, const bool elide_zero_values=false)

void	set (const size_type row, const std::vector< size_type > &col_indices, const std::vector< PetscScalar > &values, const bool elide_zero_values=false)

void	set (const size_type row, const size_type n_cols, const size_type col_indices, const PetscScalar values, const bool elide_zero_values=false)

void	add (const size_type i, const size_type j, const PetscScalar value)

void	add (const std::vector< size_type > &indices, const FullMatrix< PetscScalar > &full_matrix, const bool elide_zero_values=true)

void	add (const std::vector< size_type > &row_indices, const std::vector< size_type > &col_indices, const FullMatrix< PetscScalar > &full_matrix, const bool elide_zero_values=true)

void	add (const size_type row, const std::vector< size_type > &col_indices, const std::vector< PetscScalar > &values, const bool elide_zero_values=true)

void	add (const size_type row, const size_type n_cols, const size_type col_indices, const PetscScalar values, const bool elide_zero_values=true, const bool col_indices_are_sorted=false)

void	clear_row (const size_type row, const PetscScalar new_diag_value=0)

void	clear_rows (const std::vector< size_type > &rows, const PetscScalar new_diag_value=0)

void	compress (const VectorOperation::values operation)

PetscScalar	operator() (const size_type i, const size_type j) const

PetscScalar	el (const size_type i, const size_type j) const

PetscScalar	diag_element (const size_type i) const

size_type	m () const

size_type	n () const

size_type	local_size () const

std::pair< size_type, size_type >	local_range () const

bool	in_local_range (const size_type index) const

size_type	n_nonzero_elements () const

size_type	row_length (const size_type row) const

PetscReal	l1_norm () const

PetscReal	linfty_norm () const

PetscReal	frobenius_norm () const

PetscScalar	matrix_norm_square (const VectorBase &v) const

PetscScalar	matrix_scalar_product (const VectorBase &u, const VectorBase &v) const

PetscScalar	trace () const

MatrixBase &	operator*= (const PetscScalar factor)

MatrixBase &	operator/= (const PetscScalar factor)

MatrixBase &	add (const PetscScalar factor, const MatrixBase &other)

MatrixBase &	add (const MatrixBase &other, const PetscScalar factor)

void	vmult (VectorBase &dst, const VectorBase &src) const

void	Tvmult (VectorBase &dst, const VectorBase &src) const

void	vmult_add (VectorBase &dst, const VectorBase &src) const

void	Tvmult_add (VectorBase &dst, const VectorBase &src) const

PetscScalar	residual (VectorBase &dst, const VectorBase &x, const VectorBase &b) const

const_iterator	begin () const

const_iterator	end () const

const_iterator	begin (const size_type r) const

const_iterator	end (const size_type r) const

	operator Mat () const

Mat &	petsc_matrix ()

void	transpose ()

PetscBool	is_symmetric (const double tolerance=1.e-12)

PetscBool	is_hermitian (const double tolerance=1.e-12)

void	write_ascii (const PetscViewerFormat format=PETSC_VIEWER_DEFAULT)

void	print (std::ostream &out, const bool alternative_output=false) const

std::size_t	memory_consumption () const

Public Member Functions inherited from Subscriptor
	Subscriptor ()

	Subscriptor (const Subscriptor &)

	Subscriptor (Subscriptor &&) noexcept

virtual	~Subscriptor ()

Subscriptor &	operator= (const Subscriptor &)

Subscriptor &	operator= (Subscriptor &&) noexcept

void	subscribe (std::atomic< bool > *const validity, const std::string &identifier="") const

void	unsubscribe (std::atomic< bool > *const validity, const std::string &identifier="") const

unsigned int	n_subscriptions () const

template<typename StreamType >
void	list_subscribers (StreamType &stream) const

void	list_subscribers () const

template<class Archive >
void	serialize (Archive &ar, const unsigned int version)

Private Member Functions
void	do_reinit (const unsigned int m, const unsigned int n, const unsigned int local_rows, const unsigned int local_columns)

Static Private Member Functions
static int	matrix_free_mult (Mat A, Vec src, Vec dst)

Private Attributes
MPI_Comm	communicator

Additional Inherited Members
Public Types inherited from PETScWrappers::MatrixBase
using	const_iterator = MatrixIterators::const_iterator

using	size_type = types::global_dof_index

using	value_type = PetscScalar

Static Public Member Functions inherited from PETScWrappers::MatrixBase
static ::ExceptionBase &	ExcSourceEqualsDestination ()

static ::ExceptionBase &	ExcWrongMode (int arg1, int arg2)

Static Public Member Functions inherited from Subscriptor
static ::ExceptionBase &	ExcInUse (int arg1, std::string arg2, std::string arg3)

static ::ExceptionBase &	ExcNoSubscriber (std::string arg1, std::string arg2)

Protected Member Functions inherited from PETScWrappers::MatrixBase
void	prepare_action (const VectorOperation::values new_action)

void	assert_is_compressed ()

void	prepare_add ()

void	prepare_set ()

void	mmult (MatrixBase &C, const MatrixBase &B, const VectorBase &V) const

void	Tmmult (MatrixBase &C, const MatrixBase &B, const VectorBase &V) const

Protected Attributes inherited from PETScWrappers::MatrixBase
Mat	matrix

VectorOperation::values	last_action

Detailed Description

Implementation of a parallel matrix class based on PETSc MatShell matrix-type. This base class implements only the interface to the PETSc matrix object, while all the functionality is contained in the matrix-vector multiplication which must be reimplemented in derived classes.

This interface is an addition to the MatrixFree class to realize user-defined matrix-classes together with PETSc solvers and functionalities. See also the documentation of MatrixFree class and step-37 and step-48.

Similar to other matrix classes in namespaces PETScWrappers and PETScWrappers::MPI, the MatrixFree class provides the usual matrix-vector multiplication vmult(VectorBase &dst, const VectorBase &src) which is pure virtual and must be reimplemented in derived classes. Besides the usual interface, this class has a matrix-vector multiplication vmult(Vec &dst, const Vec &src) taking PETSc Vec objects, which will be called by matrix_free_mult(Mat A, Vec src, Vec dst) registered as matrix-vector multiplication of this PETSc matrix object. The default implementation of the vmult function in the base class wraps the given PETSc vectors with the PETScWrappers::VectorBase class and then calls the usual vmult function with the usual interface.

Author: Wolfgang Bangerth, Martin Steigemann, 2012

Definition at line 60 of file petsc_matrix_free.h.

Constructor & Destructor Documentation

◆ MatrixFree() [1/5]

MatrixFree< dim, Number >::MatrixFree ( )

Default constructor. Create an empty matrix object.

Definition at line 28 of file petsc_matrix_free.cc.

◆ MatrixFree() [2/5]

MatrixFree< dim, Number >::MatrixFree	(	const MPI_Comm &	communicator,
		const unsigned int	m,
		const unsigned int	n,
		const unsigned int	local_rows,
		const unsigned int	local_columns
	)

Create a matrix object of dimensions m times n with communication happening over the provided communicator.

For the meaning of the local_rows and local_columns parameters, see the PETScWrappers::MPI::SparseMatrix class documentation.

As other PETSc matrices, also the matrix-free object needs to have a size and to perform matrix vector multiplications efficiently in parallel also local_rows and local_columns. But in contrast to PETSc::SparseMatrix classes a PETSc matrix-free object does not need any estimation of non_zero entries and has no option is_symmetric.

Definition at line 37 of file petsc_matrix_free.cc.

◆ MatrixFree() [3/5]

MatrixFree< dim, Number >::MatrixFree	(	const MPI_Comm &	communicator,
		const unsigned int	m,
		const unsigned int	n,
		const std::vector< unsigned int > &	local_rows_per_process,
		const std::vector< unsigned int > &	local_columns_per_process,
		const unsigned int	this_process
	)

Create a matrix object of dimensions m times n with communication happening over the provided communicator.

As other PETSc matrices, also the matrix-free object needs to have a size and to perform matrix vector multiplications efficiently in parallel also local_rows and local_columns. But in contrast to PETSc::SparseMatrix classes a PETSc matrix-free object does not need any estimation of non_zero entries and has no option is_symmetric.

Definition at line 49 of file petsc_matrix_free.cc.

◆ MatrixFree() [4/5]

MatrixFree< dim, Number >::MatrixFree	(	const unsigned int	m,
		const unsigned int	n,
		const unsigned int	local_rows,
		const unsigned int	local_columns
	)

Constructor for the serial case: Same function as MatrixFree(), see above, with communicator = MPI_COMM_WORLD.

Definition at line 71 of file petsc_matrix_free.cc.

◆ MatrixFree() [5/5]

MatrixFree< dim, Number >::MatrixFree	(	const unsigned int	m,
		const unsigned int	n,
		const std::vector< unsigned int > &	local_rows_per_process,
		const std::vector< unsigned int > &	local_columns_per_process,
		const unsigned int	this_process
	)

Constructor for the serial case: Same function as MatrixFree(), see above, with communicator = MPI_COMM_WORLD.

Definition at line 82 of file petsc_matrix_free.cc.

Member Function Documentation

◆ reinit() [1/4]

void MatrixFree< dim, Number >::reinit	(	const MPI_Comm &	communicator,
		const unsigned int	m,
		const unsigned int	n,
		const unsigned int	local_rows,
		const unsigned int	local_columns
	)

Throw away the present matrix and generate one that has the same properties as if it were created by the constructor of this class with the same argument list as the present function.

Definition at line 104 of file petsc_matrix_free.cc.

◆ reinit() [2/4]

void MatrixFree< dim, Number >::reinit	(	const MPI_Comm &	communicator,
		const unsigned int	m,
		const unsigned int	n,
		const std::vector< unsigned int > &	local_rows_per_process,
		const std::vector< unsigned int > &	local_columns_per_process,
		const unsigned int	this_process
	)

Throw away the present matrix and generate one that has the same properties as if it were created by the constructor of this class with the same argument list as the present function.

Definition at line 122 of file petsc_matrix_free.cc.

◆ reinit() [3/4]

void MatrixFree< dim, Number >::reinit	(	const unsigned int	m,
		const unsigned int	n,
		const unsigned int	local_rows,
		const unsigned int	local_columns
	)

Call the reinit() function above with communicator = MPI_COMM_WORLD.

Definition at line 147 of file petsc_matrix_free.cc.

◆ reinit() [4/4]

void MatrixFree< dim, Number >::reinit	(	const unsigned int	m,
		const unsigned int	n,
		const std::vector< unsigned int > &	local_rows_per_process,
		const std::vector< unsigned int > &	local_columns_per_process,
		const unsigned int	this_process
	)

Call the reinit() function above with communicator = MPI_COMM_WORLD.

Definition at line 158 of file petsc_matrix_free.cc.

◆ clear()

void MatrixFree< dim, Number >::clear ( )

Release all memory and return to a state just like after having called the default constructor.

Definition at line 175 of file petsc_matrix_free.cc.

◆ get_mpi_communicator()

const MPI_Comm & MatrixFree< dim, Number >::get_mpi_communicator ( ) const

inlineoverridevirtual

Return a reference to the MPI communicator object in use with this matrix.

Implements PETScWrappers::MatrixBase.

Definition at line 294 of file petsc_matrix_free.h.

◆ vmult() [1/2]

virtual void PETScWrappers::MatrixFree::vmult	(	VectorBase &	dst,
		const VectorBase &	src
	)		const

pure virtual

Matrix-vector multiplication: let dst = M*src with M being this matrix.

Source and destination must not be the same vector.

Note that if the current object represents a parallel distributed matrix (of type PETScWrappers::MPI::SparseMatrix), then both vectors have to be distributed vectors as well. Conversely, if the matrix is not distributed, then neither of the vectors may be.

◆ Tvmult()

virtual void PETScWrappers::MatrixFree::Tvmult	(	VectorBase &	dst,
		const VectorBase &	src
	)		const

pure virtual

Matrix-vector multiplication: let dst = M^T*src with M being this matrix. This function does the same as vmult() but takes the transposed matrix.

Source and destination must not be the same vector.

Note that if the current object represents a parallel distributed matrix then both vectors have to be distributed vectors as well. Conversely, if the matrix is not distributed, then neither of the vectors may be.

◆ vmult_add()

virtual void PETScWrappers::MatrixFree::vmult_add	(	VectorBase &	dst,
		const VectorBase &	src
	)		const

pure virtual

Adding Matrix-vector multiplication. Add M*src on dst with M being this matrix.

Source and destination must not be the same vector.

Note that if the current object represents a parallel distributed matrix then both vectors have to be distributed vectors as well. Conversely, if the matrix is not distributed, then neither of the vectors may be.

◆ Tvmult_add()

virtual void PETScWrappers::MatrixFree::Tvmult_add	(	VectorBase &	dst,
		const VectorBase &	src
	)		const

pure virtual

Adding Matrix-vector multiplication. Add M^T*src to dst with M being this matrix. This function does the same as vmult_add() but takes the transposed matrix.

Source and destination must not be the same vector.

Note that if the current object represents a parallel distributed matrix then both vectors have to be distributed vectors as well. Conversely, if the matrix is not distributed, then neither of the vectors may be.

◆ vmult() [2/2]

void MatrixFree< dim, Number >::vmult	(	Vec &	dst,
		const Vec &	src
	)		const

virtual

The matrix-vector multiplication called by matrix_free_mult(). This function can be reimplemented in derived classes for efficiency. The default implementation copies the given vectors into PETScWrappers::*Vector and calls vmult(VectorBase &dst, const VectorBase &src) which is purely virtual and must be reimplemented in derived classes.

Definition at line 187 of file petsc_matrix_free.cc.

◆ matrix_free_mult()

int MatrixFree< dim, Number >::matrix_free_mult	(	Mat	A,
		Vec	src,
		Vec	dst
	)

staticprivate

Callback-function registered as the matrix-vector multiplication of this matrix-free object called by PETSc routines. This function must be static and takes a PETSc matrix A, and vectors src and dst, where dst = A*src

Source and destination must not be the same vector.

This function calls vmult(Vec &dst, const Vec &src) which should be reimplemented in derived classes.

Definition at line 200 of file petsc_matrix_free.cc.

◆ do_reinit()

void MatrixFree< dim, Number >::do_reinit	(	const unsigned int	m,
		const unsigned int	n,
		const unsigned int	local_rows,
		const unsigned int	local_columns
	)

private

Do the actual work for the respective reinit() function and the matching constructor, i.e. create a matrix object. Getting rid of the previous matrix is left to the caller.

Definition at line 219 of file petsc_matrix_free.cc.

Member Data Documentation

◆ communicator

MPI_Comm PETScWrappers::MatrixFree::communicator

private

Copy of the communicator object to be used for this parallel matrix- free object.

Definition at line 261 of file petsc_matrix_free.h.

The documentation for this class was generated from the following files:

deal.II/lac/petsc_matrix_free.h
source/lac/petsc_matrix_free.cc

Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MatrixFree() [1/5]

◆ MatrixFree() [2/5]

◆ MatrixFree() [3/5]

◆ MatrixFree() [4/5]

◆ MatrixFree() [5/5]

Member Function Documentation

◆ reinit() [1/4]

◆ reinit() [2/4]

◆ reinit() [3/4]

◆ reinit() [4/4]

◆ clear()

◆ get_mpi_communicator()

◆ vmult() [1/2]

◆ Tvmult()

◆ vmult_add()

◆ Tvmult_add()

◆ vmult() [2/2]

◆ matrix_free_mult()

◆ do_reinit()

Member Data Documentation

◆ communicator